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Crystal structure of the E. coli thiM riboswitch in complex with thiamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HOJ PDB ENTRY 2HOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 30% PEG2000, 0.35 M ammonium chloride, 50 mM succinate/KOH, pH 7.0, 10 mM zinc chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.503 α = 90 b = 61.503 β = 90 c = 103.935 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2012-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.99999 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.05 30 99.9 0.164 12.9 11.3 4410
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.1 99.1 0.696 8.4 214
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2HOJ 3.05 30 4200 435 94.2 0.2488 0.2488 0.3229 0.3325 109.686
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 11.793 11.793 -23.586
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.115 c_scbond_it 1.892 c_angle_d 1.062 c_bond_d 0.006 c_mcbond_it c_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1582 Solvent Atoms 4 Heterogen Atoms 24
Software Software Software Name Purpose SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction PHASER phasing